Re: The correct topology/parameter file and pgn

From: S.K. Ghosh (
Date: Wed Jun 04 2008 - 13:48:41 CDT

Hi NAMD users,

I have received the attached topology file for biotin.

But I am getting the following errors when I am using this file to run
psfgen to create the psf for biotin-streptavidin.

ERROR! Failed to parse autogenerate statement. duplicate residue key BTN
will be ignored ERROR! Explicit exclusions or fluctuating charges not
supported, atom ignored. ......

I think this is because the topology file is not in CHARMM format.

The pgn file that I am using contains:

package require psfgen
topology top_all27_prot_lipid.inp
topology btn.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment SA {pdb strepA.pdb}
coordpdb strepA.pdb SA
segment SB {pdb strepB.pdb}
coordpdb strepB.pdb SB
segment SC {pdb strepC.pdb}
coordpdb strepC.pdb SC
segment SD {pdb strepD.pdb}
coordpdb strepD.pdb SD
segment BA {pdb btnA.pdb}
coordpdb btnA.pdb BA
segment BB {pdb btnB.pdb}
coordpdb btnB.pdb BB
segment BC {pdb btnC.pdb}
coordpdb btnC.pdb BC
segment BD {pdb btnD.pdb}
coordpdb btnD.pdb BD
writepdb bs.pdb
writepsf bs.psf

StrepA is just the ATOM records for segment A of protein from the pdb file
for streptavidin-biotin from pdb database and likewise btnA is just HETATM
records for one biotin molecule from the same pdb file.

If this is due to improper format, may I get the ff top and par files for
biotin in CHARMM format please.

Look forward to getting your help.

Thanks very much.

On Jun 4 2008, Peter Freddolino wrote:

>You should be receiving parameters for biotin from the people in our
>group who worked on it a few years ago shortly (if they haven't arrived
>S.K. Ghosh wrote:
>> Hi Peter,
>> Thanks very much.
>> This psfgen is giving errors because the pdb file is for
>> streptavidin-biotin and the topology file is only for protein. So I
>> need CHARMM topology and parameter files for Biotin. Could someone
>> help me with suggestions where I could find these.
>> Thanks very much.
>> Sourav
>> On Jun 3 2008, Peter Freddolino wrote:
>>> Hi Sourav,
>>> the parameters from the namd tutorial should be the same as the ones
>>> you mention from MacKerell's website; you can always use diff or a
>>> similar tool to confirm this.
>>> In your psfgen input script, you appear to be missing the underscores
>>> in the topology file name. Also, segment NAME {pdb blah} and coordpdb
>>> blah NAME are separate statements and thus should go on separate
>>> lines. You will also need to modify that psfgen script if you have
>>> anything unusual in your protein (disulfide bonds, etc.). It's best
>>> to look at the structure after running psfgen to verify that it
>>> appears chemically correct.
>>> Best,
>>> Peter
>>> S.K. Ghosh wrote:
>>>> Dear NAMD Users,
>>>> I am a newbie in NAMD simulations. Could you please suggest which
>>>> parameter/topology file should ideally be used for a simulation of
>>>> biotin-streptavidin in water, where I am using 1swe.pdb
>>>> (streptavidin complex with biotin).
>>>> Are the topology and parameter files used in the NAMD tutorial
>>>> examples (par_all27_prot_lipid.inp and top_all27_prot_lipid.inp)
>>>> same as par_all27_prot_lipid.rtf and top_all27_prot_lipid.rtf on Dr
>>>> Mackerell's website?
>>>> Also, the pdb files available from RCSB Protein Databank do not
>>>> contain H atoms. So I do not need to remove the H atoms, as is done
>>>> in the tutorial for ubbiquitin. Could you please confirm this.
>>>> Finally, to create the psf file and NAMD compatible pdb file (with
>>>> H) for biotin-streptavidin, is it OK if I run the following .pgn file.
>>>> package require psfgen
>>>> topology top all27 prot lipid.inp
>>>> pdbalias residue HIS HSE
>>>> pdbalias atom ILE CD1 CD
>>>> segment BS {pdb 1swe.pdb} coordpdb 1swe.pdb BS
>>>> guesscoord
>>>> writepdb bs.pdb
>>>> writepsf bs.psf
>>>> Your suggestions will be immensely helpful.
>>>> Thanks very much.
>>>> Sourav

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